Aberrant expression of genes plays significant roles in the pathogenesis or pathological alterations in cancer, endocrine-related disorders, immune/inflammatory diseases, genetic diseases, and neurological diseases. The human genome is packaged into chromatin that consists of DNA, histones and non-histone proteins. Chromatin structure is an important factor in determining whether a particular gene is expressed or not. In general, condensed chromatin mediates transcriptional repression, whereas transcriptionally active genes are in areas of open chromatin. Nucleosomes form the basic repeating unit of chromatin, and consist of DNA wrapped around a histone octomer that is formed by four histone partners, namely an H3-H4 tetramer and two H2A-H2B dimers. Histone H1 acts like a linker to stabilize the higher-order folding by electrostatic neutralization of the linker DNA segments through a positively charged carboxy-terminal domain. Therefore, the dynamic higher-order structure of nucleosomes defines distinct levels of chromatin organization and consequently, gene activation. Ricky W. Johnstone, “Histone deacetylase inhibitors: novel drugs for the treatment of cancer”, Nature Reviews Drug Discovery 2002, 1: 287. The capacity of histone octomer to compact DNA is influenced by a number of post-translational modifications that occur on the N-terminal histone tails. One modification involves the reversible acetylation and deacetylation of the epsilon-amino group of lysine moieties found within the histone tails. The net level of acetylation of N-terminal histone tails is controlled by the activities of two families of enzymes, the histone acetyltransferases (HATS) and histone deacetylases (HDACs). In addition to HATs and HDACs, other factors also participate in determination of chromatin structure, including methyl-CpG-binding protein and adenosine triphosphate-dependent chromatin-remodeling complexes that can directly recruit HDACs, which leads to repression of gene activation (see review Current Opinion in Oncology 2001, 13:477-483).
The identification of coactivator complexes that possess intrinsic HAT activity strongly supports the connection between histone acetylation and transcriptional activation. Similarly, transcriptional repressor complexes have been shown to recruit HDACs to the promoter of target genes (Bioassays 1998, 20:615). Sequence-specific transcription factors, such as nuclear hormone receptor super-family, cyclic adenosine 3′,5′-monophosphate-related enhancer binding protein (CREB), and signal transducer and activator of transcription-1 (STAT-1), interact with distinct coactivators and corepressors inside the complex of transcriptional machinery in a DNA-context and tissue-context selective fashion, resulting in selective regulation of gene expression networks. These regulatory networks govern homeostasis of our body's physiological functions and perturbation of those networks causes disorders and/or profoundly affects progression of diseases. Therefore, modulation of complex interactions of transcription machinery provides novel intervention strategies for the treatments of cancer, endocrine-related disorders, immune/inflammatory diseases, genetic diseases, and neurodegeneration (Korzus, E., et al., Transcription Factor-specific Requirements for Coactivator and Their Acetyltransferase Functions. Science 1998, 279:703-707; McKenna, N. J. and B. W. O'Malley, Combinatorial Control of Gene Expression by Nuclear Receptors and Coregulators. Cell 2002, 108(4):465-474; Pazin, M. J. and J. T. Kadonaga, What's Up and Down with Histone Deacetylation and Transcription? Cell 1997, 89(3):325-328; Zhong, H., R. E. Voll, and S. Ghosh, Phosphorylation of NF-B p65 by PKA Stimulates Transcriptional Activity by Promoting a Novel Bivalent Interaction with the Coactivator CBP/p300. Molecular Cell 1998, 1(5):661-671; Steffan J. S. et al., Histone deacetylase inhibitors arrest polyglutamine-dependent neurodegeneration in Drosophila, Nature 2001, 413:691-694; HDAC inhibitor VX-563 from Vertex Pharmaceuticals proceeds for genetic disorders, 2002 EDGAR online News, US20020115716A1, WO0056153A1).
For instance, cell development and differentiation are governed by the hierarchical order of sequential gene activation, which is controlled at the level of chromatin structure. Genetic alterations or mutations that cause constitutive activation of oncoproteins such as RAS, or inactivation of tumor suppressors such as p53, affect a myriad of molecular programs, including transcription. In addition, genetic abnormalities that result in improper targeting of HATs and HDACs to certain loci, functional inactivation of HATs, overexpression of HDACs or epigenetic changes due to DNA hyper- and hypomethylation, can shift balance between cell development and differential programs that often lead to tumor onset and progression (see review Current Opinion Genet. Development 1999, 9:40-48 and 175-184). Several human cancers have been associated with malfunctions in HAT and HDAC activity. One example is the translocation of chromosomes 15 and 17 seen in the majority of acute promyelocytic leukemia (APL) patients. In APL, chromosomal translocations produce fusion proteins that contain RARalpha, PML (promyelocytic leukaemia protein), and PLZF (promyelocytic zinc finger). These aberrant proteins bind to retinoic acid response elements, recruit HDACs with high affinity through enhanced binding for SMRT corepressor and are not responsive to retinoids, resulting in the constitutive repression of RAR-targeted genes (Oncogene 2001, 20:7204-7215). Retinoid acid receptor (RAR) is a ligand-activated transcriptional modulator that is important for myeloid differentiation. RAR heterodimerized with its partner RXR binds to retinoid acid response element, located in promoter region of target genes, and in the absence of retinoids, represses transcription by recruiting SIN3/HDAC through NCOR and SMRT corepressors. Addition of ligand releases the HDAC complexes from RAR/RXR, and allows subsequent binding of HATs, such as TIF2 and CBP, to activate transcription. Therefore the coordinated activation and repression of genes that contain functional retinoid acid response elements is essential to myeloid cell differentiation. Furthermore, addition of HDAC inhibitors can restore sensitivity of APL cells to retinoid-induced myeloid cell differentiation, indicating that aberrant histone deacetylation is a key process in leukaemogenesis.
There are reports that histone deacetylases, when overexpressed, silence the expression of tumor suppressor genes that are natural brakes against tumor growth. For example, p53, a critical regulator of cell proliferation, transmits signals to genes that control the cell cycle and apoptosis when cells are under stress. The functions are principally controlled by the ability of p53 to bind to DNA with sequence-specificity and to activate transcription. Inactivation of this property of p53, mostly by mutations that occur in the central DNA-binding domain, often leads to malignancy. It has been demonstrated that CBP/p300 can up-regulate p53 through core histone acetylation and p53 acetylation. (W. Gu and R. G Roeder, Activation of p53 Sequence-Specific DNA Binding by Acetylation of the p53 C-Terminal Domain. Cell 1997, 90(4): 595-606.) Conversely, mammalian HDAC-1, HDAC-2, and HDAC-3 are shown to be capable of downregulating p53 function by deacetylation of both core histone and p53 (Juan, L.-J., et al., Histone Deacetylases Specifically Down-regulate p53-dependent Gene Activation. The Journal of Biological Chemistry 2000, 275(27):20436-20443).
These data show that inappropriate transcriptional repression mediated by HDACs is a common molecular mechanism that is used by oncoproteins, and alterations in chromatin structure can impinge on normal cellular differentiation, which leads to tumor formation and other hyper-proliferative disorders. Therefore, the inhibition of HDAC activity seems to be a rational therapeutic pathway for cancers and other hyperproliferative diseases.
Several classes of HDAC inhibitors have been identified, including (1) short-chain fatty acids, e.g. butyrate and phenylbutyrate; (2) organic hydroxamic acids, e.g. suberoylanilide hydroxamic acid (SAHA) and trichostatin A (TSA); (3) cyclic tetrapeptides containing a 2-amino-8-oxo 9,10-expoxydecanoyl (AOE) moiety, e.g. trapoxin and HC-toxin; (4) cyclic peptides without the AOE moiety, e.g. apicidin and FK228; and (5) benzamides, e.g. MS-275 (EP0847992A1, US2002/0103192A1, WO02/26696A1, WO01/70675A2, WO01/18171A2).
Butyric acid acts as an inhibitor of cell proliferation and an inducer of cytodifferentiation due primarily to its activity of inhibiting histone deacetylase. (A. Nudelman and A. Rephaeli, Novel Mutual Prodrug of Retinoic and Butyric Acids with Enhanced Anticancer Activity. J. Med. Chem. 2000, 43(15):2962-2966.) Phenylbutyrate has been used as a single agent in the treatment of β-thalassemia, toxoplasmosis, and malaria. It is also reported to be successful in treating refractory APL in combination with RA (retinoid acid). (R. P. Warrell et al., Therapeutic targeting of transcription in acute promyelocytic leukemia by use of an inhibitor of histone deacetylase. J. Natl. Cancer Inst. 1998, 90(21):1621-1625.) Another fatty acid, valproic acid, which is a potent anticonvulsant, mood stabilizer and teratogen, is also a direct inhibitor of histone deacetylase. (C. J. Phiel et al., Histone Deacetylase Is a Direct Target of Valproic Acid, a Potent Anticonvulsant, Mood Stabilizer, and Teratogen. The Journal of Biological Chemistry 2001, 276(39): 36734-36741; EP 170008A1).
A set of benzamides was discovered to have HDAC inhibitory activity in the low micromolar range. A lead compound, MS-275, from this set of benzamides is being tested by Mitsui Chemicals, Inc. and it is the first HDAC inhibitor to demonstrate oral anticancer activity in animal models with no severe side effects. (A. Saito et al., A synthetic inhibitor of histone deacetylase, MS-27-275, with marked in vivo antitumor activity against human tumors. Proceedings of the National Academy of Sciences of the United States of America 1999, 96(8): 4592-4597; EP 0847992 A1). MS-275 is currently under clinical trials in the University of Maryland Greenebaum Cancer Center for leukemia patients and by the U.S. National Cancer Institute for advanced solid tumors. (E. B. Levit, Clinical Trials in Leukemia focus on New Treatment Approaches. 2001 Release—University of Maryland Medical News 2001 Maryland http://www.umm.edu/news/releases/karp.html, A Phase I Study of an Oral Histone Deacetylase Inhibitor, MS-275, in Refractory Solid Tumors and Lymphomas. 2001, National Cancer Institute). However, there is still a need to discover new compounds with improved profiles, such as stronger HDAC inhibitory activity.